Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps).

Neha S Gandhi,Pilar Blancafort,Ricardo L Mancera

doi:10.18632/oncotarget.25025

Abstract

The neural-specific transcription factor Engrailed 1 - is overexpressed in basal-like breast tumours. Synthetic interference peptides - comprising a cell-penetrating peptide/nuclear localisation sequence and the Engrailed 1-specific sequence from the N-terminus have been engineered to produce a strong apoptotic response in tumour cells overexpressing EN1, with no toxicity to normal or non Engrailed 1-expressing cells. Here scaled molecular dynamics simulations were used to study the conformational dynamics of these interference peptides in aqueous solution to characterise their structure and dynamics. Transitions from disordered to α-helical conformation, stabilised by hydrogen bonds and proline-aromatic interactions, were observed throughout the simulations. The backbone of the wild-type peptide folds to a similar conformation as that found in ternary complexes of anterior Hox proteins with conserved hexapeptide motifs important for recognition of pre-B-cell leukemia Homeobox 1, indicating that the motif may possess an intrinsic preference for helical structure. The predicted NMR chemical shifts of these peptides are consistent with the Hox hexapeptides in solution and Engrailed 2 NMR data. These findings highlight the importance of aromatic residues in determining the structure of Engrailed 1 interference peptides, shedding light on the rational design strategy of molecules that could be adopted to inhibit other transcription factors overexpressed in other cancer types, potentially including other transcription factor families that require highly conserved and cooperative protein–protein partnerships for biological activity.

Highlights

Studies of breast carcinomas have established the role of transcription factors to be highly expressed in cancers and as drivers of cancer initiation, disease recurrence and resistance to treatment [1]
A turn conformation is observed preceding the hexapeptide motif, which is very stable in the simulation of the shorter Engrailed 1 (EN1)-iPep 2 (i.e. Peptide 2)
Simulation of Peptide 3 revealed a tendency to fold into beta strands, such that the hexapeptide motif forms a bend-turn resulting in a β-hairpin structure (Figure 1C)

Summary

Introduction

Studies of breast carcinomas have established the role of transcription factors (notably those that contain developmental homoedomains) to be highly expressed in cancers and as drivers of cancer initiation, disease recurrence and resistance to treatment [1]. The functional significance of the overexpression of Engrailed members in cancers, basal-like breast cancers, has recently been highlighted [3]. Transcription factors, unlike other molecular cancer targets, have largely remained “undruggable” due to a lack of small molecular binding pockets. Interference www.oncotarget.com peptides (EN1-iPeps) that selectively inhibit EN1 activity have offered a novel route for the treatment of aggressive basal-like triple negative breast carcinomas. The nanoparticle-encapsulated iPep has been selectively targeted to basal-like cancerous cells in combination with anti-cancer drug docetaxel and doxorubicin to produce a highly synergistic pharmacological activity [4]

Methods

Results

Conclusion